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coding style and whitespace cleanup to match LAMMPS style

This commit is contained in:
Axel Kohlmeyer 2017-07-05 12:33:41 -04:00
parent 9fa4588eb7
commit 6eddc1a2ee
3 changed files with 271 additions and 281 deletions
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66
src/USER-MISC/fix_wall_ees.cpp
View File

@ -11,13 +11,25 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "math.h" /* ----------------------------------------------------------------------
Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include "math_extra.h" #include "math_extra.h"
#include "fix_wall_ees.h" #include "fix_wall_ees.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h" #include "error.h"
#include "math_extra.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
@ -96,13 +108,13 @@ void FixWallEES::wall_particle(int m, int which, double coord)
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (side < 0) if (side < 0)
delta = x[i][dim] - coord; delta = x[i][dim] - coord;
else else
delta = coord - x[i][dim]; delta = coord - x[i][dim];
if (delta >= cutoff[m]) if (delta >= cutoff[m])
continue; continue;
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}}; double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
double tempvec[3]= {0,0,0}; double tempvec[3]= {0,0,0};
@ -168,37 +180,37 @@ void FixWallEES::wall_particle(int m, int which, double coord)
hms = delta - sigman; hms = delta - sigman;
fwall = side*( fwall = side*(
-1*coeff4[m]/hhss2 + -1*coeff4[m]/hhss2 +
coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8 coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
); );
f[i][dim] -= fwall; f[i][dim] -= fwall;
ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) + ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7; coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
ewall[m+1] += fwall; ewall[m+1] += fwall;
twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) + twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ; coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
MathExtra::matvec(Lx,nhat,tempvec); MathExtra::matvec(Lx,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2); MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k]; for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[0] = MathExtra::dot3(SAn,tempvec2); that[0] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Ly,nhat,tempvec); MathExtra::matvec(Ly,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2); MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k]; for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[1] = MathExtra::dot3(SAn,tempvec2); that[1] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Lz,nhat,tempvec); MathExtra::matvec(Lz,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2); MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k]; for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
that[2] = MathExtra::dot3(SAn,tempvec2); that[2] = MathExtra::dot3(SAn,tempvec2);
for(int j = 0; j<3 ; j++) for(int j = 0; j<3 ; j++)
tor[i][j] += twall * that[j]; tor[i][j] += twall * that[j];
} }

478
src/USER-MISC/fix_wall_region_ees.cpp
View File

@ -1,4 +1,4 @@
/* -*- c++ -*- ---------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
@ -10,10 +10,14 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <iostream>
#include "math.h" /* ----------------------------------------------------------------------
#include "stdlib.h" Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
#include "string.h" ------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_wall_region_ees.h" #include "fix_wall_region_ees.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
@ -31,117 +35,109 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
enum{LJ93,LJ126,COLLOID,HARMONIC,EES};//me
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
/// USAGE:
/// fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff
///
FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) : FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) Fix(lmp, narg, arg)
{ {
if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command"); if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
scalar_flag = 1; scalar_flag = 1;
vector_flag = 1; vector_flag = 1;
size_vector = 3; size_vector = 3;
global_freq = 1; global_freq = 1;
extscalar = 1; extscalar = 1;
extvector = 1; extvector = 1;
// parse args // parse args
iregion = domain->find_region(arg[3]); iregion = domain->find_region(arg[3]);
if (iregion == -1) if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region/ees does not exist"); error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
int n = strlen(arg[3]) + 1; int n = strlen(arg[3]) + 1;
idregion = new char[n]; idregion = new char[n];
strcpy(idregion,arg[3]); strcpy(idregion,arg[3]);
epsilon = force->numeric(FLERR,arg[4]);
sigma = force->numeric(FLERR,arg[5]);
cutoff = force->numeric(FLERR,arg[6]);
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
epsilon = force->numeric(FLERR,arg[4]); eflag = 0;
sigma = force->numeric(FLERR,arg[5]); ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
cutoff = force->numeric(FLERR,arg[6]);
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixWallRegionEES::~FixWallRegionEES() FixWallRegionEES::~FixWallRegionEES()
{ {
delete [] idregion; delete [] idregion;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
int FixWallRegionEES::setmask() int FixWallRegionEES::setmask()
{ {
int mask = 0; int mask = 0;
mask |= POST_FORCE; mask |= POST_FORCE;
mask |= THERMO_ENERGY; mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA; mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE; mask |= MIN_POST_FORCE;
return mask; return mask;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixWallRegionEES::init() void FixWallRegionEES::init()
{ {
// set index and check validity of region // set index and check validity of region
iregion = domain->find_region(idregion); iregion = domain->find_region(idregion);
if (iregion == -1) if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region/ees does not exist"); error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix wall/region/ees requires extended particles");
// setup coefficients
coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
offset = 0;
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); if (strstr(update->integrate_style,"respa"))
if (!avec) nlevels_respa = ((Respa *) update->integrate)->nlevels;
error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix wall/region/ees requires extended particles");
// setup coefficients for each style
coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
offset = 0;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixWallRegionEES::setup(int vflag) void FixWallRegionEES::setup(int vflag)
{ {
if (strstr(update->integrate_style,"verlet")) if (strstr(update->integrate_style,"verlet"))
post_force(vflag); post_force(vflag);
else { else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0); post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
} }
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -155,121 +151,111 @@ void FixWallRegionEES::min_setup(int vflag)
void FixWallRegionEES::post_force(int vflag) void FixWallRegionEES::post_force(int vflag)
{ {
//me //sth is needed here, but I dont know what
//sth is needed here, but I dont know what //that is calculation of sn
//that is calculation of sn
int i,m,n; int i,m,n;
double rinv,fx,fy,fz,tooclose[3];//me double rinv,fx,fy,fz,sn,tooclose[3];
double sn;//me
eflag = 0; eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0; ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
double *radius = atom->radius; double **tor = atom->torque;
double **tor = atom->torque; //me AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");//me int *mask = atom->mask;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;//me int nlocal = atom->nlocal;
int *ellipsoid = atom->ellipsoid;//me
int *mask = atom->mask; Region *region = domain->regions[iregion];
int nlocal = atom->nlocal; region->prematch();
Region *region = domain->regions[iregion]; int onflag = 0;
region->prematch();
int onflag = 0; // region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= radius is an error
// region->match() insures particle is in region or on surface, else error for (i = 0; i < nlocal; i++)
// if returned contact dist r = 0, is on surface, also an error if (mask[i] & groupbit) {
// in COLLOID case, r <= radius is an error if (!region->match(x[i][0],x[i][1],x[i][2])) {
onflag = 1;
continue;
}
for (i = 0; i < nlocal; i++) double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
if (mask[i] & groupbit) { double tempvec[3]= {0,0,0};
if (!region->match(x[i][0],x[i][1],x[i][2])) { double sn2 = 0.0;
onflag = 1; double nhat[3] = {0,0,0};
continue; double* shape = bonus[ellipsoid[i]].shape;;
} MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}}; for(int which = 0 ; which < 3; which ++){//me
double tempvec[3]= {0,0,0}; nhat[which]=1;
double sn2 = 0.0; nhat[(which+1)%3] = 0 ;
double nhat[3] = {0,0,0}; nhat[(which+2)%3] = 0 ;
double* shape = bonus[ellipsoid[i]].shape;; sn2 = 0 ;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A); MathExtra::transpose_matvec(A,nhat,tempvec);
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
sn = sqrt(sn2);
tooclose[which] = sn;
}
for(int which = 0 ; which < 3; which ++){//me n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
nhat[which]=1;
nhat[(which+1)%3] = 0 ;
nhat[(which+2)%3] = 0 ;
sn2 = 0 ;
MathExtra::transpose_matvec(A,nhat,tempvec);
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
sn = sqrt(sn2);
tooclose[which] = sn;
}
for (m = 0; m < n; m++) {
if (region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0]){
onflag = 1;
continue;
} else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
onflag = 1;
continue;
} else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
onflag = 1;
continue;
} else rinv = 1.0/region->contact[m].r;
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff); ees(m,i);
for (m = 0; m < n; m++) { ewall[0] += eng;
fx = fwall * region->contact[m].delx * rinv;
fy = fwall * region->contact[m].dely * rinv;
fz = fwall * region->contact[m].delz * rinv;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
if(region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0] ){ ewall[1] -= fx;
onflag = 1; ewall[2] -= fy;
continue; ewall[3] -= fz;
}else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){ tor[i][0] += torque[0];
onflag = 1; tor[i][1] += torque[1];
continue; tor[i][2] += torque[2];
}else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){ }
onflag = 1; }
continue;
}
else rinv = 1.0/region->contact[m].r;
ees(m,i);//me if (onflag) error->one(FLERR,"Particle on or inside surface of region "
"used in fix wall/region/ees");
ewall[0] += eng;
fx = fwall * region->contact[m].delx * rinv;
fy = fwall * region->contact[m].dely * rinv;
fz = fwall * region->contact[m].delz * rinv;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
ewall[1] -= fx;
ewall[2] -= fy;
ewall[3] -= fz;
tor[i][0] += torque[0];
tor[i][1] += torque[1];
tor[i][2] += torque[2];
}
}
if (onflag) error->one(FLERR,"Particle on or inside surface of region "
"used in fix wall/region/ees");
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop) void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
{ {
if (ilevel == nlevels_respa-1) post_force(vflag); if (ilevel == nlevels_respa-1) post_force(vflag);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixWallRegionEES::min_post_force(int vflag) void FixWallRegionEES::min_post_force(int vflag)
{ {
post_force(vflag); post_force(vflag);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -278,13 +264,13 @@ void FixWallRegionEES::min_post_force(int vflag)
double FixWallRegionEES::compute_scalar() double FixWallRegionEES::compute_scalar()
{ {
// only sum across procs one time // only sum across procs one time
if (eflag == 0) { if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1; eflag = 1;
} }
return ewall_all[0]; return ewall_all[0];
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -293,18 +279,15 @@ double FixWallRegionEES::compute_scalar()
double FixWallRegionEES::compute_vector(int n) double FixWallRegionEES::compute_vector(int n)
{ {
// only sum across procs one time // only sum across procs one time
if (eflag == 0) { if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1; eflag = 1;
} }
return ewall_all[n+1]; return ewall_all[n+1];
} }
//me
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
EES interaction for ellipsoid particle with wall EES interaction for ellipsoid particle with wall
compute eng and fwall and twall = magnitude of wall force and torque compute eng and fwall and twall = magnitude of wall force and torque
@ -312,94 +295,89 @@ double FixWallRegionEES::compute_vector(int n)
void FixWallRegionEES::ees(int m, int i) void FixWallRegionEES::ees(int m, int i)
{ {
Region *region = domain->regions[iregion]; Region *region = domain->regions[iregion];
region->prematch(); region->prematch();
double delta = 0.0, delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0; double delta, delta2, delta3, delta4, delta5, delta6;
double sigman = 0.0, sigman2 = 0.0 , sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0; double sigman, sigman2 , sigman3, sigman4, sigman5, sigman6;
double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0; //h^2 - s_n^2 double hhss, hhss2, hhss4, hhss7, hhss8; //h^2 - s_n^2
double hps = 0.0; //h+s_n double hps; //h+s_n
double hms = 0.0; //h-s_n double hms; //h-s_n
double twall = 0.0; double twall;
double tempvec[3]={0,0,0};
double tempvec2[3]= {0,0,0};
double SAn[3] = {0,0,0}; double A[3][3], nhat[3], SAn[3], that[3];
double that[3] = {0,0,0};
double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}}; double tempvec[3]= {0,0,0};
double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}}; double tempvec2[3]= {0,0,0};
double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}}; double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}};
double nhat[3] = {0,0,0}; double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}};
double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
nhat[0] = region->contact[m].delx / region->contact[m].r; nhat[0] = region->contact[m].delx / region->contact[m].r;
nhat[1] = region->contact[m].dely / region->contact[m].r; nhat[1] = region->contact[m].dely / region->contact[m].r;
nhat[2] = region->contact[m].delz / region->contact[m].r; nhat[2] = region->contact[m].delz / region->contact[m].r;
//avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); AtomVecEllipsoid::Bonus *bonus = avec->bonus;
AtomVecEllipsoid::Bonus *bonus = avec->bonus; int *ellipsoid = atom->ellipsoid;
int *ellipsoid = atom->ellipsoid;//me
double* shape = bonus[ellipsoid[i]].shape;; double* shape = bonus[ellipsoid[i]].shape;;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A); MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
MathExtra::transpose_matvec(A,nhat,tempvec); sigman2 = 0.0;
for(int k = 0; k<3; k++) tempvec[k] *= shape[k]; MathExtra::transpose_matvec(A,nhat,tempvec);
for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k]; for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
for(int k = 0; k<3; k++) SAn[k] = tempvec[k]; for(int k = 0; k<3; k++) sigman2 += tempvec[k]*tempvec[k];
for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
sigman = sqrt(sigman2);
delta = fabs(region->contact[m].r);
sigman = sqrt(sigman2); sigman3 = sigman2 * sigman;
delta = fabs(region->contact[m].r); sigman4 = sigman2 * sigman2;
sigman5 = sigman4 * sigman;
sigman6 = sigman3 * sigman3;
sigman3 = sigman2 * sigman; delta2 = delta * delta;
sigman4 = sigman2 * sigman2; delta3 = delta2 * delta;
sigman5 = sigman4 * sigman; delta4 = delta2 * delta2;
sigman6 = sigman3 * sigman3; delta5 = delta3 * delta2;
delta6 = delta3 * delta3;
delta2 = delta * delta; hhss = delta2 - sigman2;
delta3 = delta2 * delta; hhss2 = hhss * hhss;
delta4 = delta2 * delta2; hhss4 = hhss2 * hhss2;
delta5 = delta3 * delta2; hhss8 = hhss4 * hhss4;
delta6 = delta3 * delta3; hhss7 = hhss4 * hhss2 * hhss;
hhss = delta2 - sigman2; hps = delta + sigman;
hhss2 = hhss * hhss; hms = delta - sigman;
hhss4 = hhss2 * hhss2;
hhss8 = hhss4 * hhss4;
hhss7 = hhss4 * hhss2 * hhss;
hps = delta + sigman; fwall = -1*coeff4/hhss2 + coeff3
hms = delta - sigman; * (21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6) / hhss8;
fwall = -1*coeff4/hhss2 + eng = -1*coeff2 * (4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3) +
coeff3 * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8 coeff1 * (35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4) / hhss7;
;
eng = -1*coeff2 * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) + twall = coeff6 * (6*delta3/sigman4/hhss2 - 10*delta/sigman2/hhss2
coeff1 * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7; + 3*log(hms/hps)/sigman5)
+ coeff5 * (21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4) / hhss8;
twall = coeff6 * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) + MathExtra::matvec(Lx,nhat,tempvec);
coeff5 * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ; MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[0] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Lx,nhat,tempvec); MathExtra::matvec(Ly,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2); MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k]; for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[0] = MathExtra::dot3(SAn,tempvec2); that[1] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Ly,nhat,tempvec); MathExtra::matvec(Lz,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2); MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k]; for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
that[1] = MathExtra::dot3(SAn,tempvec2); that[2] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Lz,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
that[2] = MathExtra::dot3(SAn,tempvec2);
for(int j = 0; j<3 ; j++)
torque[j] = twall * that[j];
for(int j = 0; j<3 ; j++)
torque[j] = twall * that[j];
} }

8
src/USER-MISC/fix_wall_region_ees.h
View File

@ -40,7 +40,7 @@ class FixWallRegionEES : public Fix {
double compute_vector(int); double compute_vector(int);
private: private:
class AtomVecEllipsoid *avec;//me class AtomVecEllipsoid *avec;
int iregion; int iregion;
double epsilon,sigma,cutoff; double epsilon,sigma,cutoff;
@ -50,11 +50,11 @@ class FixWallRegionEES : public Fix {
char *idregion; char *idregion;
double coeff1,coeff2,coeff3,coeff4,offset; double coeff1,coeff2,coeff3,coeff4,offset;
double coeff5, coeff6;//me double coeff5, coeff6;
double eng,fwall; double eng,fwall;
double torque[3];//me double torque[3];
void ees(int, int);//me void ees(int, int);
}; };
} }